The spending plan calls for a 10-percent cut to all state agencies across the board, including the court system, the health department and $1 billion slashed from Medicaid funding. Cuomo's plan to lay off nearly 10,000 in state workers still remains uncertain.

The budget will restore $22 million for prescriptions for the elderly and $86 million for SUNY hospitals and colleges, including Stony Brook. Cuomo also restored $272 million in school aid, which was in jeopardy of being cut by more than $1 billion.

Political consultant Mike Dawidziak sees the agreement as a huge victory for the governor, and not a bad deal for Nassau and Suffolk counties.

"Long Island's going to suffer just like all the regions of the state are going to suffer. But what I think is significant about this, is that Long Island isn't going to suffer more pain at a higher price than New York City, for example," Dawidziak says.